TABLE 1.
Primers used in this study
| Assay type and gene target | Primer | Sequence | Product size (kb)a | Source and/or referenceb |
|---|---|---|---|---|
| Single-target PCRc | ||||
| mecA | mecAF | 5′-CTTTGCTAGAGTAGCACTCG-3′ | ||
| mecAR | 5′-GCTAGCCATTCCTTTATCTTG-3′ | 0.5 | 13 | |
| mecA | mecAaminoF | 5′-AGTTGTAGTTGTCGGGTTTGG-3′ | ||
| mecAaminoR | 5′-GGGACCAACATAACCTAATAGAT-3′ | 0.74 | This study | |
| mecI | mI3 | 5′-CAAAAGGACTGGAGTCCAAA-3′ | ||
| mI4 | 5′-CAAGTGAATTGAAACCGCCT-3′ | 0.18 | 38 | |
| mecR1 (MS) | mcR3 | 5′-ATCTCCACGTTAATTCCATT-3′ | ||
| mcR4 | 5′-GTCGTTCATTAAGATATGACG-3′ | 0.3 | 38 | |
| mecR1 (PB) | mcR1 | 5′-CGCTCAGAAATTTGTTGTGC-3′ | ||
| mcR5 | 5′-CAGGGAATGAAAATTATTGGA-3 | 0.32 | 38 | |
| mec complex C2d | IS-5 | 5′-CTGCATCAATGGCACGATATAA-3′ | 5.5 | This study |
| orfX | orfXprobeF | 5′-GGAAGCAAGCCATAGCAGAA-3′ | ||
| orfXprobeR | 5′-TGCTTCTCCACGCATAATCTT-3′ | 0.4 | This study | |
| ccrAB4 | ccrA4-F | 5′-ATGGGATAAGAGAAAAAGCC-3′ | ||
| ccrB4-R | 5′-TAATTTACCTTCGTTGGCAT-3′ | 1.4 | This study | |
| ccrC | γFg | 5′-CGTCTATTACAAGATGTTAAGGATAAT-3′ | 16 | |
| γR | 5′-CCTTTATAGACTGGATTATTCAAAATAT-3′ | 0.5h | 16 | |
| CDS15-R | 5′-GTATGCGGGTTGTTCTTGTTCAT-3′ | 2.2h | This study | |
| VT uniquee | ccrC-FR | 5′-CCAACAAATTAAAGCAAAACAAGC-3′ | 4.0 | This study |
| PVL locus | PVL-1 | 5′-CTGGTGCGATTCATGGTA-3′ | ||
| PVL-2 | 5′-CGATATCGTGGTCATCACA-3′ | 3.5 | 2.5 | |
| Multiplex PCR | ||||
| Multiplef | β2 | 5′-ATTGCCTTGATAATAGCCITCT-3′ | 15; this study | |
| ccrAB1 | α2 | 5′-AACCTATATCATCAATCAGTACAT-3′ | 0.7i | 15; this study |
| ccrAB2 | α3 | 5′-TAAAGGCATCAATGCACAAACACT-3′ | 1.0i | 15; this study |
| ccrAB3 | α4 | 5′-AGCTCAAAAGCAAGCAATAGAAT-3′ | 1.6i | 15; this study |
Predicted size of PCR product when the indicated reverse primer is used in conjunction with the given forward primer.
The reference or source is for both the forward and the reverse primers. A reference is given for the forward primer only if it was used with more than one reverse primer, and one is also given for each single primer. For the multiplex PCR, the primers were described previously, and the assay conditions are described in this study.
For each gene target, the first primer listed is the forward primer, and the subsequent primer listed is the reverse primer.
Only a single primer is required because the mec complex C2 is flanked by complementary inverted repeats of 15431.
This target is a unique product of SCCmec VT that is formed when this primer is used alone.
The multiplex PCR involved the use of one forward universal primer (β2) with three reverse primers (α2, α3, and α4) to target multiple genes. The individual targets are listed with their respective reverse primers.
The forward primer γF was used with two reverse primers (γR and CDS15-R) to target the same gene.
Product size when this reverse primer is used in conjunction with γF.
Product size when this reverse primer is used in conjunction with β2.